incorporating inchiinto a polymeric database · polymer dictionary module proposed polymer-t gpairs...
TRANSCRIPT
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Incorporating InChI intoa polymeric database
Debra J. AudusState and Future of the IUPAC InChIAugust 16, 2017
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Acknowledgements
Roselyne Tchoua Kyle Chard Logan Ward Ian Foster
Jian Qin Joshua Lequieu Juan de Pablo
Computer Science
Molecular Engineering
Chemical Engineering
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Need for polymeric databases
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Existing resourcesPaper-based Web-based
limited accessibility of entire database and/or datasets that are too small
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Polymer Property Predictorand Database
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Flory Huggins χ parameter
Publications
R.B. Tchoua, J. Qin, D.J. Audus, et al. J. Chem. Educ., 93, 1561-1568 (2016)R.B. Tchoua, K. Chard, D.J. Audus, et al. Procedia Comp. Sci., 80, 386-397 (2016)
376 articles from Macromolecules
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Flory Huggins χ parameter
InformationExtraction ModulePublications
1
R.B. Tchoua, J. Qin, D.J. Audus, et al. J. Chem. Educ., 93, 1561-1568 (2016)R.B. Tchoua, K. Chard, D.J. Audus, et al. Procedia Comp. Sci., 80, 386-397 (2016)
Automatically extract metadata (title, author, etc.)
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Flory Huggins χ parameter
InformationExtraction ModulePublications Proposed
χ EntriesData ParsingCrowdsourcingModule
1
2
R.B. Tchoua, J. Qin, D.J. Audus, et al. J. Chem. Educ., 93, 1561-1568 (2016)R.B. Tchoua, K. Chard, D.J. Audus, et al. Procedia Comp. Sci., 80, 386-397 (2016)
TgTgχ
Undergrads review papers and enter χ into an online form
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Need for a polymer dictionaryName Type Abbreviationpoly(ethylene-alt-propylene) polymer PEPprotonated poly(ethylene-alt-propylene) polymer pPEPPolybutadiene polymerpolybutadiene polymer PBpolybutadiene polymer PBDpoly(butyl methacrylate) polymer PbMAPoly(n-butyl methacrylate) polymer PnBMA-115 poly(methacrylic acid)-b-poly(methyl methacrylate) (A) polymer PMAA-PMMA (A)poly(methacrylic acid)-b-poly(methyl methacrylate) (C) polymer PMAA-PMMA (C)styrene polymer
prefixes
capitalization
input errors
ambiguous
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The need for InChIMultiple and trade names Identify synonyms
Broadness of CAS
poly(2,6-dimethyl-1,4-phenylene oxide)poly(xylenyl ether)
1800+for polystyrene
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Need for a polymer dictionaryName Type Abbreviationpoly(ethylene-alt-propylene) polymer PEPprotonated poly(ethylene-alt-propylene) polymer pPEPPolybutadiene polymerpolybutadiene polymer PBpolybutadiene polymer PBDpoly(butyl methacrylate) polymer PbMAPoly(n-butyl methacrylate) polymer PnBMA-115 poly(methacrylic acid)-b-poly(methyl methacrylate) (A) polymer PMAA-PMMA (A)poly(methacrylic acid)-b-poly(methyl methacrylate) (C) polymer PMAA-PMMA (C)styrene polymer
prefixes
capitalization
input errors
ambiguous
Need something like PubChem for polymers
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Flory Huggins χ parameter
InformationExtraction ModulePublications
…poly(styrene) polyethylenepolyisoprene….
CuratedPolymerDictionaryModule
Proposedχ EntriesData ParsingCrowdsourcingModule
1
3
2
R.B. Tchoua, J. Qin, D.J. Audus, et al. J. Chem. Educ., 93, 1561-1568 (2016)R.B. Tchoua, K. Chard, D.J. Audus, et al. Procedia Comp. Sci., 80, 386-397 (2016)
TgTgχ
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Developing the polymer dictionaryName
InChIKey and InChI
poly(2-vinylpyridine)
Abbreviation
P2VP
Structure(saved as .mol file)
KGIGUEBEKRSTEW-BBVYVPKKBA-N
1B/C7H7N/c1-2-7-5-3-4-6-8-7/h2-6H,1H2/z101-1-8(1.2)
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The polymer dictionary
88 entries 3 without InChI associated .mol files
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Flory Huggins χ parameter
InformationExtraction ModulePublications
…poly(styrene) polyethylenepolyisoprene….
CuratedPolymerDictionaryModule
Proposedχ Entries
Confirmedχ Entries
Data ParsingCrowdsourcingModule
1
3
2
FinalExpertReview
4pppdb
R.B. Tchoua, J. Qin, D.J. Audus, et al. J. Chem. Educ., 93, 1561-1568 (2016)R.B. Tchoua, K. Chard, D.J. Audus, et al. Procedia Comp. Sci., 80, 386-397 (2016)
TgTgχ
TgTgχ
Final review and push to database
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Glass transition temperature
Publications
R.B. Tchoua, K. Chard, D.J. Audus, et al. submitted to 13th IEEE International Conference on e-Science
6,090 articles from Macromolecules
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Glass transition temperatureNaturalLanguageProcessingModulePublications
1
R.B. Tchoua, K. Chard, D.J. Audus, et al. submitted to 13th IEEE International Conference on e-Science
Tries to find compound-Tg pairs automatically
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Glass transition temperatureNaturalLanguageProcessingModulePublications
…PS 25Polystyrene 25poly(styrene) 25PMMA 26….
NLPPolymerDictionaryModule
1
2
R.B. Tchoua, K. Chard, D.J. Audus, et al. submitted to 13th IEEE International Conference on e-Science
Automatically create a dictionary of polymers
(only names) using“P” and “poly”
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NLP Polymer DictionaryNamePolystyrenepoly(styrene)polystyrenepolystyrenesPSPSSpolyimidespolyolefincopolymer 10poly(2,4’-BF-a)macroporous poly(N-isopropylacrylamide)gel
various forms
not plural of PS
labels not names
family names
prefixes/suffixes
12,814 polymers in the dictionary
Work in progress to clean up errors above and adding InChI
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Glass transition temperatureNaturalLanguageProcessingModulePublications
Compound-TgPairs
SolitaryTgs
Label-TgPairs
PrioritizeReviewModule
TgTgTgTgTg
TheTgofPEOpeaksatamolecularweightof6000(Tg=−17°C)….
PolymerProximitySearchModule
TgTgTg
…PS 25Polystyrene 25poly(styrene) 25PMMA 26….
NLPPolymerDictionaryModule
ProposedPolymer-Tg Pairs
P TgP TgP Tg
P TgP TgP Tg
ConfirmedPolymer-Tg Pairs
Untrained
P TgP TgP TgPX TgResolve
ResolveLabelCrowdsourcingModule
FlagBadDataCrowdsourcingModule
1
4 5
TgCandidates
2
P TgP TgP TgP TgC Tg
…PS 25Polystyrene 25….
PolymerIdentificationModule
3
FinalExpertReview
6pppdb
R.B. Tchoua, K. Chard, D.J. Audus, et al. submitted to 13th IEEE International Conference on e-Science
Many other steps to final product!
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The need for InChIMultiple and trade names Identify synonyms
Broadness of CAS Input/output for machine learning
NaturalLanguageProcessing Module
1
poly(2,6-dimethyl-1,4-phenylene oxide)poly(xylenyl ether)
1800+for polystyrene
1B/C8H8O/c1-5-3-7-46(2)8(5)9-7/h3-4H,12H3/z101-1-9(7,9,8,9)
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Limitations of current InChIBranching / crosslinksOrganometallic
Markush
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Conclusions and outlook
http://pppdb.uchicago.edu263 χ 258 Tg
Future work• Add .mol files and InChI to pppdb• Cleaning up NLP polymer dictionary
Advances still need for InChI• Organometallics• Branching / cross-links• Markush
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Flory Huggins χ parameter
InformationExtraction ModulePublications
…poly(styrene) polyethylenepolyisoprene….
CuratedPolymerDictionaryModule
Proposedχ Entries
Confirmedχ Entries
Data ParsingCrowdsourcingModule
1
3
2
FinalExpertReview
4pppdb
R.B. Tchoua, J. Qin, D.J. Audus, et al. J. Chem. Educ., 93, 1561-1568 (2016)R.B. Tchoua, K. Chard, D.J. Audus, et al. Procedia Comp. Sci., 80, 386-397 (2016)
TgTgχ
TgTgχ
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Glass transition temperatureNaturalLanguageProcessingModulePublications
Compound-TgPairs
SolitaryTgs
Label-TgPairs
PrioritizeReviewModule
TgTgTgTgTg
TheTgofPEOpeaksatamolecularweightof6000(Tg=−17°C)….
PolymerProximitySearchModule
TgTgTg
…PS 25Polystyrene 25poly(styrene) 25PMMA 26….
NLPPolymerDictionaryModule
ProposedPolymer-Tg Pairs
P TgP TgP Tg
P TgP TgP Tg
ConfirmedPolymer-Tg Pairs
Untrained
P TgP TgP TgPX TgResolve
ResolveLabelCrowdsourcingModule
FlagBadDataCrowdsourcingModule
1
4 5
TgCandidates
2
P TgP TgP TgP TgC Tg
…PS 25Polystyrene 25….
PolymerIdentificationModule
3
FinalExpertReview
6pppdb
R.B. Tchoua, K. Chard, D.J. Audus, et al. submitted to 13th IEEE International Conference on e-Science